AMBER Archive (2007)

Subject: AMBER: replica exchange

From: Geoff Wood (geoffrey.wood_at_epfl.ch)
Date: Sun Oct 28 2007 - 10:29:42 CST

Dear Amber users,

I am interested in utilizing a Blugene/L machine that I have
available to me. I successfully compiled and ran PMEMD calculations
on the BG/L using the config files available from the following link
http://amber.scripps.edu/config.bgl.html however, I have just
realised that remd is not implement in PMEMD. Is there a way of
including the routines in multisander in the PMEMD compilation or
compiling sander from scratch using similar config files? I don't
think sander will have scaling problems on a BG/L when using remd
because although you could utilize many cpus it is the number of cpus
per replica that counts.

Kind regards

Dr Geoffrey Wood
Ecole Polytechnique Fédérale de Lausanne
SB - ISIC - LCBC
BCH 4108
CH - 1015 Lausanne

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